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- PDB-5yit: Crystal Structure of Hypothetical protein (Rv3272) from Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 5yit
TitleCrystal Structure of Hypothetical protein (Rv3272) from Mycobacterium tuberculosis
ComponentsCoA transferase III
KeywordsTRANSFERASE / CoA transferase Family III / interlocked dimer / Mycobacterium tuberculosis / Rv3272
Function / homologyTransferases; Transferring sulfur-containing groups; CoA-transferases / : / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / transferase activity / Probable fatty acyl-CoA transferase Rv3272
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsKarade, S.S. / Pratap, J.V.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Rv3272 encodes a novel Family III CoA transferase that alters the cell wall lipid profile and protects mycobacteria from acidic and oxidative stress.
Authors: Karade, S.S. / Pandey, S. / Ansari, A. / Das, S. / Tripathi, S. / Arora, A. / Chopra, S. / Pratap, J.V. / Dasgupta, A.
History
DepositionOct 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CoA transferase III
B: CoA transferase III
C: CoA transferase III
D: CoA transferase III
E: CoA transferase III


Theoretical massNumber of molelcules
Total (without water)212,5275
Polymers212,5275
Non-polymers00
Water2,576143
1
A: CoA transferase III
B: CoA transferase III


Theoretical massNumber of molelcules
Total (without water)85,0112
Polymers85,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-84 kcal/mol
Surface area26470 Å2
MethodPISA
2
C: CoA transferase III
D: CoA transferase III


Theoretical massNumber of molelcules
Total (without water)85,0112
Polymers85,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-81 kcal/mol
Surface area26650 Å2
MethodPISA
3
E: CoA transferase III

E: CoA transferase III


Theoretical massNumber of molelcules
Total (without water)85,0112
Polymers85,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10670 Å2
ΔGint-80 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)542.400, 71.000, 49.550
Angle α, β, γ (deg.)90.00, 90.44, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16B
26E
17C
27D
18C
28E
19D
29E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUAA6 - 3916 - 391
21PROPROLEULEUBB6 - 3916 - 391
12ASNASNLEULEUAA5 - 3915 - 391
22ASNASNLEULEUCC5 - 3915 - 391
13ASNASNPHEPHEAA5 - 3905 - 390
23ASNASNPHEPHEDD5 - 3905 - 390
14PROPROLEULEUBB6 - 3916 - 391
24PROPROLEULEUCC6 - 3916 - 391
15PROPROPHEPHEBB6 - 3906 - 390
25PROPROPHEPHEDD6 - 3906 - 390
16PROPROVALVALBB6 - 3896 - 389
26PROPROVALVALEE6 - 3896 - 389
17ASNASNPHEPHECC5 - 3905 - 390
27ASNASNPHEPHEDD5 - 3905 - 390
18PROPROVALVALCC6 - 3896 - 389
28PROPROVALVALEE6 - 3896 - 389
19PROPROVALVALDD6 - 3896 - 389
29PROPROVALVALEE6 - 3896 - 389

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.226724, -0.973914, 0.009409), (-0.973952, 0.226677, -0.00584), (0.003555, -0.010488, -0.999939)132.05688, 105.1132, 36.26708
3given(0.94819, -0.317665, -0.004977), (0.317672, 0.9482, 0.000801), (0.004465, -0.00234, 0.999987)44.73596, 8.95089, 9.00563
4given(-0.520532, -0.853794, 0.009066), (-0.853841, 0.52052, -0.003866), (-0.001418, -0.009753, -0.999951)113.03493, 63.5233, 27.20017
5given(-0.785528, -0.618786, 0.007011), (-0.618815, 0.785531, -0.002958), (-0.003677, -0.006662, -0.999971)83.66774, 30.78293, 18.14123

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Components

#1: Protein
CoA transferase III


Mass: 42505.445 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv3272 / Production host: Escherichia coli (E. coli) / References: UniProt: P96877
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.2 %
Description: Plate shaped crystals grown overnight at room temperature
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100mM Tris-HCl, 100mM MgCl2, 20-25% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9858 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 25, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9858 Å / Relative weight: 1
ReflectionResolution: 2.79→43.59 Å / Num. obs: 45755 / % possible obs: 96.88 % / Redundancy: 3.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1032 / Net I/σ(I): 7.86
Reflection shellResolution: 2.79→2.89 Å / Redundancy: 2.97 % / Rmerge(I) obs: 0.3565 / Mean I/σ(I) obs: 2.97 / Num. unique obs: 4303 / CC1/2: 0.92 / % possible all: 79.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VJQ

2vjq


Resolution: 2.79→43.59 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: THROUGHOUT / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28578 2260 4.9 %RANDOM
Rwork0.23124 ---
obs0.23387 43495 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.566 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20.17 Å2
2--2.13 Å20 Å2
3----1.43 Å2
Refinement stepCycle: 1 / Resolution: 2.79→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12467 0 0 143 12610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01912702
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.94917374
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.36251732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.1424.332494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.796151688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9251574
X-RAY DIFFRACTIONr_chiral_restr0.1020.22044
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0219825
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6086.5676991
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.3039.8338702
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.496.3235709
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.81560.46152225
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A6460.22
12B6460.22
21A6200.22
22C6200.22
31A6640.24
32D6640.24
41B6960.21
42C6960.21
51B7200.21
52D7200.21
61B6860.24
62E6860.24
71C7000.22
72D7000.22
81C6600.22
82E6600.22
91D6880.24
92E6880.24
LS refinement shellResolution: 2.792→2.864 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 119 -
Rwork0.309 2478 -
obs--75.82 %

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